Bottom Line:
We analyse the distribution of mitochondrial translation initiation factors and their sequence features, given two well-propagated claims: first, a sequence insertion in mitochondrial IF2 (mIF2) compensates for the universal lack of IF1 in mitochondria, and secondly, no homologue of mitochondrial IF3 (mIF3) is identifiable in Saccharomyces cerevisiae.Our comparative sequence analysis shows that, in fact, the mIF2 insertion is highly variable and restricted in length and primary sequence conservation to vertebrates, while phylogenetic and in vivo complementation analyses reveal that an uncharacterized S. cerevisiae mitochondrial protein currently named Aim23p is a bona fide evolutionary and functional orthologue of mIF3.Our results highlight the lineage-specific nature of mitochondrial translation and emphasise that comparative analyses among diverse taxa are essential for understanding whether generalizations from model organisms can be made across eukaryotes.

Affiliation: University of Tartu, Institute of Technology, Tartu, Estonia. gemma.atkinson@ut.ee

ABSTRACTMitochondrial translation is essentially bacteria-like, reflecting the bacterial endosymbiotic ancestry of the eukaryotic organelle. However, unlike the translation system of its bacterial ancestors, mitochondrial translation is limited to just a few mRNAs, mainly coding for components of the respiratory complex. The classical bacterial initiation factors (IFs) IF1, IF2 and IF3 are universal in bacteria, but only IF2 is universal in mitochondria (mIF2). We analyse the distribution of mitochondrial translation initiation factors and their sequence features, given two well-propagated claims: first, a sequence insertion in mitochondrial IF2 (mIF2) compensates for the universal lack of IF1 in mitochondria, and secondly, no homologue of mitochondrial IF3 (mIF3) is identifiable in Saccharomyces cerevisiae. Our comparative sequence analysis shows that, in fact, the mIF2 insertion is highly variable and restricted in length and primary sequence conservation to vertebrates, while phylogenetic and in vivo complementation analyses reveal that an uncharacterized S. cerevisiae mitochondrial protein currently named Aim23p is a bona fide evolutionary and functional orthologue of mIF3. Our results highlight the lineage-specific nature of mitochondrial translation and emphasise that comparative analyses among diverse taxa are essential for understanding whether generalizations from model organisms can be made across eukaryotes.

gks272-F1: Phylogenetic tree of mitochondrial IF2 (mIF2), bacterial IF2 and chloroplast IF2 (cpIF2). The tree is a MrBayes consensus tree, generated from 405 aligned amino acids. The standard deviation of split frequencies at the end of the MrBayes run was 0.018. Bayesian inference posterior probability (BIPP) and maximum likelihood bootstrap percentage (MLBP) support are indicated on branches. Only branches with >0.70 BIPP support are labelled with BIPP and MLPP values. The scale bar below the tree shows the evolutionary distance expressed as substitutions per site. Numbers in taxon names are NCBI GI numbers. Vertical blocks show the distribution of IF1, mitochondrial IF1 (mIF1), chloroplast IF1 (cpIF1), IF3, mitochondrial IF3 (mIF3), Aim23p and chloroplast IF3 (cpIF3). Blocks in the same column indicate orthologous proteins. The black bracket shows the taxonomic boundary of the full-length conserved animal IF2 insertion.

Mentions:
The full IF2 data set comprises alignment columns that are universally alignable across the IF2 family of bacteria, archaea and eukaryotes. Reducing the data set to the bacterial and organellar IF2 group alone and removing the long-branched protist sequences means more positions can be used, and LBA artefacts minimized. Phylogenetic analysis of this cut-down IF2 data set shows much more resolution of the organellar sequences (Figure 1). There is strong support (1.0 BIPP, 90% MLBP) for the monophyly of mIF2 and also full support (1.0 BIPP, 100% MLBP) for the grouping of cpIF2 with cyanobacteria.Figure 1.

gks272-F1: Phylogenetic tree of mitochondrial IF2 (mIF2), bacterial IF2 and chloroplast IF2 (cpIF2). The tree is a MrBayes consensus tree, generated from 405 aligned amino acids. The standard deviation of split frequencies at the end of the MrBayes run was 0.018. Bayesian inference posterior probability (BIPP) and maximum likelihood bootstrap percentage (MLBP) support are indicated on branches. Only branches with >0.70 BIPP support are labelled with BIPP and MLPP values. The scale bar below the tree shows the evolutionary distance expressed as substitutions per site. Numbers in taxon names are NCBI GI numbers. Vertical blocks show the distribution of IF1, mitochondrial IF1 (mIF1), chloroplast IF1 (cpIF1), IF3, mitochondrial IF3 (mIF3), Aim23p and chloroplast IF3 (cpIF3). Blocks in the same column indicate orthologous proteins. The black bracket shows the taxonomic boundary of the full-length conserved animal IF2 insertion.

Mentions:
The full IF2 data set comprises alignment columns that are universally alignable across the IF2 family of bacteria, archaea and eukaryotes. Reducing the data set to the bacterial and organellar IF2 group alone and removing the long-branched protist sequences means more positions can be used, and LBA artefacts minimized. Phylogenetic analysis of this cut-down IF2 data set shows much more resolution of the organellar sequences (Figure 1). There is strong support (1.0 BIPP, 90% MLBP) for the monophyly of mIF2 and also full support (1.0 BIPP, 100% MLBP) for the grouping of cpIF2 with cyanobacteria.Figure 1.

Bottom Line:
We analyse the distribution of mitochondrial translation initiation factors and their sequence features, given two well-propagated claims: first, a sequence insertion in mitochondrial IF2 (mIF2) compensates for the universal lack of IF1 in mitochondria, and secondly, no homologue of mitochondrial IF3 (mIF3) is identifiable in Saccharomyces cerevisiae.Our comparative sequence analysis shows that, in fact, the mIF2 insertion is highly variable and restricted in length and primary sequence conservation to vertebrates, while phylogenetic and in vivo complementation analyses reveal that an uncharacterized S. cerevisiae mitochondrial protein currently named Aim23p is a bona fide evolutionary and functional orthologue of mIF3.Our results highlight the lineage-specific nature of mitochondrial translation and emphasise that comparative analyses among diverse taxa are essential for understanding whether generalizations from model organisms can be made across eukaryotes.

Affiliation:
University of Tartu, Institute of Technology, Tartu, Estonia. gemma.atkinson@ut.ee

ABSTRACTMitochondrial translation is essentially bacteria-like, reflecting the bacterial endosymbiotic ancestry of the eukaryotic organelle. However, unlike the translation system of its bacterial ancestors, mitochondrial translation is limited to just a few mRNAs, mainly coding for components of the respiratory complex. The classical bacterial initiation factors (IFs) IF1, IF2 and IF3 are universal in bacteria, but only IF2 is universal in mitochondria (mIF2). We analyse the distribution of mitochondrial translation initiation factors and their sequence features, given two well-propagated claims: first, a sequence insertion in mitochondrial IF2 (mIF2) compensates for the universal lack of IF1 in mitochondria, and secondly, no homologue of mitochondrial IF3 (mIF3) is identifiable in Saccharomyces cerevisiae. Our comparative sequence analysis shows that, in fact, the mIF2 insertion is highly variable and restricted in length and primary sequence conservation to vertebrates, while phylogenetic and in vivo complementation analyses reveal that an uncharacterized S. cerevisiae mitochondrial protein currently named Aim23p is a bona fide evolutionary and functional orthologue of mIF3. Our results highlight the lineage-specific nature of mitochondrial translation and emphasise that comparative analyses among diverse taxa are essential for understanding whether generalizations from model organisms can be made across eukaryotes.